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While Thomas does not appear in his mother's household in 1841, the fact that he was born in Mevagissey and that his father was Michael Burn(s), a blacksmith, makes it definite that he was indeed the son of Michael Burns/Byrne and Jane Ley.  He must have either been living elsewhere in 1841 or mistakenly left out by the census taker.  Your Thomas appears in my article on his great-nephew Michael Cyprian O'Byrne (born Michael Burns) in The American Genealogist, 88 (2016): 241-253 (esp. 245).  Like several of his other siblings, he was baptized twice, once in the Wesleyan chapel at St. Austell and once in the Church of England church at Mevagissey (there was a good deal of religious foment in Cornwall at this time).